Another MLS team went out of the CONCACAF Champions league at the hands of a Liga MX opponent, but the Quakes were within inches of victory.
After a scoreless first half in which Toluca held the lion's share of the possession, San Jose took the lead in the game and the series with a set piece goal in the 56th minute. Shea Salinas served up a long free kick from deep, and Ty Harden nipped ahead of Wilson Tiago to hit a first-time header past Alfredo Talavera and into the net.
Isaac Brizuela brought proceedings back to level terms with a fantastic volley in the 70th minute. A Toluca corner and an ensuing cross were both cleared, but Brizuela, hanging on the edge of the area, was well-placed to smash it back in.
The match went to extra time after 90 scoreless minutes, and San Jose looked to have scored a crucial winner, but Alan Gordon was perhaps incorrectly flagged offside.
Jon Busch prevented Toluca's best extra-time chance when he pushed Wilson Tiago's effort into the crossbar before his defense cleared the ball off the line.
Toluca eventually triumphed in a penalty shootout when Salinas' effort hit the crossbar in a sudden-death round.